Molecular biology of sarcoma

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Address for correspondence:

Anna M. Czarnecka, MD, PhD Klinika Nowotworów Tkanek Miękkich, Kości i Czerniaków

Centrum Onkologii — Instytut im. Marii Skłodowskiej-Curie ul. Roentgena 5, 02–781 Warszawa Phone: +48 22 546 20 27 Fax: +48 22 643 93 75 e-mail: am.czarnecka@coi.pl

Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland

3Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland

4Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute — Oncology Centre, Warsaw, Poland

5Department of Experimental and Clinical Physiology, Warsaw Medical University, Warsaw, Poland

Molecular biology of sarcoma

ABSTRACT

Soft tissue sarcomas are a large group of heterogenous neoplasms, many of them are highly aggressive. Most of the cases are sporadic, without any well-defined pathogenetic factor. Potential risk factors are ionizing radiation, lymphatic oedema (secondary angiosarcoma of the breast), viral infections (HHV8 and Kaposi sarcoma), exposure to chemical factors (vinyl chloride and hepatic angiosarcoma). Genetic susceptibility plays a role in a minority of cases. However, mutations in TP53, ATM and ATR genes are associated with enhanced susceptibility to radiation.

Li-Fraumeni syndrome (autosomal dominant TP53 mutation) predisposes to development of malignancies, one third of them are sarcomas. Genetic alterations observed in sarcomas could be divided into three major groups characterized by: (1) chromosome translocations; (2) simple karyotype and mutations; (3) variably complex karyotypes. A large part of sarcomas belong to the first group and the specific chromosal translocations could be utilized in the diagnostic process. A smaller number of sarcomas could be assigned to the second group, e.g. desmoid fibromatosis (CTNNB1 or APC mutations) and GIST (KIT, PDGFRA, or less frequently BRAF, SDH, NF1). A large number of sarcomas are characterized by complex and variable karyotypes. Gene copy number alterations are frequent in this group, e.g. in well-differentiated liposarcoma there is an amplification of MDM2, CDK4 and HMGA2 genes or sarcoma-specific chromosomal break regions present in the CHOP gene in myxoid liposarcoma and FKHR in alveolar rhabdomyosarcoma.

Key words: sarcoma, genetics, STS Oncol Clin Pract 2018; 14, 6: 307–330

Soft tissue sarcomas account for a large group of heterogeneous mesenchymal tumours, which constitute about 1% of solid tumours in adults. Many of them are very aggressive, so they are responsible for dispro- portionately more malignancy-related deaths in young adults than cancers. Their typical classification is based on the similarity to healthy mesenchymal tissues to which the type of specific sarcoma is the closest. The term soft tissue sarcoma includes more than 70 types, and primary sarcoma consists of 12 basic types, which differ in terms of pathological and clinical features [1, 2].

In the vast majority of cases, sarcomas occur sporadi- cally, without a clearly defined factor underlying tumori- genesis. Possible risk factors include exposure to ionising radiation, lymphoedema (breast angiosarcoma), viral infections (HHV8 — Kaposi sarcoma), or exposure to chemical agents (vinyl chloride — liver angiosarcoma) [2].

Mutations in genes TP53, ATM, and ATR are associ- ated with increased sensitivity to ionising radiation and subsequent development of sarcomas [3]. In 10% of patients with type 1 neurofibromatosis (NF1, mutation in the gene encoding neurofibromin 1) gastrointestinal stromal tumours (GIST) as well as malignant peripheral nerve sheath tumours (MPNST) develop. Li-Fraumeni syndrome (autosomal dominant mutation in the TP53 gene encoding p53 tumour suppressor protein) predisposes to the development of malignant tumours, one third of them are sarcomas. Other syndromes that predispose to the development of sarcomas are Gardner syndrome (desmoid tumour), Werner syndrome (soft tissue sarcomas), Bloom’s syndrome (osteosarcoma), Beckwith-Wiedemann syndrome (rhabdomyosarcoma), and Costello syndrome (rhabdomyosarcoma). Some of the spindle cell sarcomas (SCSs) are present during the

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Recent studies on a group of 1162 patients with sar- comas suggest other genetic risk factors, such as BRCA2, ATM, ATR, and ERCC2 gene damage [3]. The early phase research centre MD Anderson Cancer Centre carried out an analysis of potential mutations in patients with soft tissue sarcomas, i.e. 102 consecutive patients directed to this centre were tested using the Foundation Medicine (FoundationOne) test based on next-genera- tion sequencing (NGS). The study included a panel of 315 genes for which targeted drugs are established. Most commonly the mutations were found in TP53 (31.4% of patients), CDK4 (23.5%), MDM2 (21.6%), RB1 (18.6%), and CDKN2A/B (13.7%) genes. Interestingly, 50% of patients receiving treatment based on the result of the test (16%) achieved stable disease (SD). Of the 102 patients in the examined cohort, 40 (39%) were characterised by either no known mutation (7%) or no mutation currently recognised as the target of the available drug (32%). The remaining 62 (61%) patients had mutations potentially allowing the use of targeted therapy. Fourteen (14%) patients had lesions that could be used for treatment with the medicinal products registered for sarcoma treatment. There were cases of treatment with pazopanib or imatinib, which included five patients with the PDGFR mutation (1 GIST), four with the FGFR mutation, three with the KIT mutation (2 GIST), and two with the KDR gene aberrations [7]. Due to the high heterogeneity of sarcomas one should expect a very wide spectrum of genome damage but also numerous epigenetic changes.

Generally, the genetic changes observed in sarcomas can be divided into three groups:

— chromosomal translocations;

— point mutations without changing the karyotype;

— the presence of a variable and complex karyotype;

The sarcomas characterised by the presence of the first group of lesions (translocations) include a significant proportion of sarcomas. Occurrence of translocations is used for diagnostic purposes (Tables 1, 2). A smaller number of cases could be included in the group of the second type of defects (point muta- tions), for example desmoid tumour (CTNNB1 or APC gene mutations) or GIST (KIT or PDGFRA mutations, significantly less BRAF, SDH, NF1). Finally, a large proportion of sarcomas are classified as the third type of lesion, which are characterised by a complex and variable karyotype. In these tumours, the number of gene copies may be much higher, such as in differentiated liposarcomas, in which the amplifications of the MDM2, CDK4, and HMGA2 genes are observed. Typical chromosomal damage can also occur, such as in CHOP gene in myxoid liposarcoma and FKHR gene in alveo- lar rhabdomyosarcoma.

206 tumours of six major types of adult sarcomas. There were five tumours with complex karyotype: (1) dedifferentiated liposarcoma (DDLPS ), (2) leiomyosarcoma (LMS), (3) undifferentiated pleomorphic sarcoma (UPS), (4) myxofibrosarcoma (MFS), (5) malignant peripheral nerve sheath tumour and sarcoma with a relatively simple karyotype, and (6) synovial sarcoma, in which a single chromosomal translocation t(X;18) (p11;q11) is typically observed. In contrast to tumours of epithelial origin, the examined sarcomas (with the exception of synovial sarcoma) are characterised pri- marily by changes in the number of gene copies, with a small overall number of point mutations (insertions, deletions, missense mutations). A high number of mu- tations occur in only a few genes (TP53, ATRX, RB1), which are “repeated” in many types of sarcomas. For example, while MDM2 amplification was present in all DDLPS, deletions in TP53 were found in 9% of LMS, 16% of UPS, and 12% of MFS. In RB path, RB1 dele- tions were detected in 14% of LMS, 16% of UPS, and 24% of MFS; and CDKN2A deletions (p16) in 8% of LMS, 20% of UPS, and 18% of MFS. The disturbances of the RB pathway also included CDK4 amplification in 86% and CDKN2A deletions in 2% of DDLPS. Gener- ally, it has been shown that the total number of somatic mutations in the aforementioned types of sarcomas are relatively low (1.06 per Mb); however, 67% of tumours carried mutations previously known as potentially on- cogenic. The highest mutation burden was identified in DDLPS and MPNST, mostly C>T mutations in the CpG islands. Only 12% of the tumours had elongated telomeres. A significant role in tumour progression of sarcomas may be played by specific changes in the DNA methylation pattern and regulation via miRNA.

In these studies, JUN gene amplification was identified as a potential marker for shorter survival and a puta- tive therapeutic target in the subgroup of DDLPS sarcomas. Although it has been found that uterine LMS (ULMS) and soft tissue LMS (STLMS) are molecularly distinct, inhibitors of the PI3K-AKT-mTOR signalling pathway may have potential application in the treatment of both sarcoma groups. STLMS were characterised by the activation of the HIF1a and IGF1R pathway, cell cy- cle (CCNE2 — G1/S-Specific Cyclin-E2), DNA replica- tion (MCM2 — minichromosome maintenance complex component 2), and DNA repair (FANCI — Fanconi anaemia group I protein) deregulation, while ULMS were mainly affected by DNA repair (ESR1 — oestrogen receptor 1) disturbances. Finally, molecular analyses have shown that UPS and MFS are tumours with the same cellular origin (a common type of progenitor cell) that have different numbers of mucosal components,

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HMGA2-CXCR7 HMGA2-EBF1 HMGA2-LHPF HMGA2-LPP HMGA2-NFIB HMGA2-PPAP2B

HMGA2-LPP LPP-C12orf9

t(2;12)(q37;q14) t(5;12)(q33;q14) t(12;13)(q14;q13) t(3;12)(q28;q14) t(9;12)(p22;q14) t(1;12)(p32;q14) t(3;6)(q27;p21) t(3;12)(q28;14)

Lipoblastoma COL1A2-PLAG1

HAS2-PLAG1 PLAG1-RAD51L1

COL3A1-PLAG1

t(7;8)(q21q12) Del(8)(q12q24) t(8;14)(q12;q24) t(2;8)(q31;q12.1)

Chondroid lipoma C11orf95-MKL2 t(11;16)(q13;p13)

Myxoid/round liposarcoma FUS-DDIT3

EWSR1-DDIT3

t(12;16)(q13;p11) t(12;22)(q13;q12)

Soft tissue angiofibroma AHRR-NCOA2

GTF2I-NCOA2

t(5;8)(p15;q13) t(7;8;14)(q11;q13;q31)

Dermatofibrosarcoma protuberans COL1A1-PDGFB t(17;22)(q21;q13)

Low-grade fibromyxoid sarcoma FUS-CREB3L2

FUS-CREB3L1 EWSR1-CREB3L1

t(7;16)(q34:p11) t(7;16)(p11;p11) t(11;22)(p11;q12)

Solitary fibrous tumour NAB2-STAT6 inv(12)(q13q13)

Infantile fibrosarcoma ETV6-NTRK3 t(12;15)(p13;q25)

Sclerosing epithelioid fibrosarcoma FUS-CREB3L2

FUS-CREB3L1 EWSR1-CREB3L1

t(7;16)(q34:p11) t(11;16)(p13;p11) t(11;22)(p11;q12) Myxoinflammatory fibroblastic sarcoma/haemosiderotic fibrolipomatous

tumour

MGEA5-TGFBR3 der(10)t(1;10)(p22;q24)

Inflammatory myofibroblastic tumour CARS-ALK

SEC31A-ALK ATIC-ALK RANBP2-ALK

CLTC-ALK TPM3-ALK TPM4-ALK PPFIBP1-ALK

RREB1-TFE3

t(2;11)(P23;P15) t(2;4)(P23;Q21) inv(2)(P23;q35) t(2;2)(p23;q13) t(2;17)(p23;q23)

t(1;2)(q21;p23) t(2;19)(p23;p13) t(2;12)(p23;p11) t(X;6)(p11;p24)

Myxofibrosarcoma KIAA2026-NUDT11

CCBL1-ARL1 AFF3-PHF1

t(9;X)(p24;p11) t(9;12)(q34;q23)

t(2;6)(q12;p21)

Tenosynovial giant cell tumour COL6A3-CSF1 t(1;2)(p13;q37)

Pericytoma with (7;12) translocation ACTB-GLI1 t(7;12)(p22;q13)

Alveolar rhabdomyosarcoma PAX3-FOXO1

PAX7-FOXO1 PAX3-FOXO4 PAX3-NCOA1 PAX3-NCOA2 FOXO1-FGFR1

t(2;13)(Q35;Q14) t(1;13)(p36;q14) t(X;2)(q13;q36) t(2;2)(p23;q36) t(2;8)(q36;q13) t(8;13;9)(p11;q14;q32)

Spindle cell rhabdomyosarcoma SRF-NCOA2

TEAD1-NCOA2 t(6;8)(p21;q13) t(8;11)(q13;p15)

Angiomatoid fibrous histiocytoma EWSR1-CREB1

FUS-ATF1 EWSR1-ATF1

t(2;22)(q33;q12) t(12;16)(q13;p11) t(12;22)(q13;q12)

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Ossifying fibromyxoid tumour EP400-PHF1 MEAF6-PHF1 ZC3H7B-BCOR

t(6;12)(p21;q24) t(1;6)(p34;p21) t(X;22)(p11;q13)

Myoepithelioma/mixed tumour EWSR1-ATF1

EWSR1-PBX1 EWSR1-POU5F1 EWSR1-ZNF444 EWSR1-KLF17

EWSR1-PBX3 FUS-KLF17 LIFR-PLAG1 SRF-E2F1

t(12;22)(Q13;q12) t(1;22)(q23;q12) t(6;22)(p21;q12) t(19;22)(q13;,q12) t(1;22)(p34.1;q12) t(9;22)(q12.2;q33.3)

t(1;16)(p34.1;p11) t(5;8)(p13;q12) t(20;6)(q11;p21)

Clear cell sarcoma EWSR1-ATF1

EWSR1-CREB1 IRX2-TERT

t(12;22)(q13;q12) t(2;22)(q33;q12)

del(5)(p15.33)

Synovial sarcoma SS18-SSX1

SS18-SSX2 SS18-SSX4 SS18L1-SSX1

t(X;18)(p11;q11) t(X;18)(p11;q11) t(X;18)(p11;q11) t(X;20)(p11;q13)

Biphenotypic sinonasal sarcoma PAX3-MAML3

PAX3-NCOA1 PAX3-FOXO1

t(2;4)(q35;q31.1) t(2;2)(q35;p.23) t(2;13)(q35;q14)

Alveolar soft part sarcoma ASPSCR1-TFE3 t(X;17)(p11;q25)

Extraskeletal myxoid chondrosarcoma EWSR1-NR4A3

TAF15-NR4A3 TFG-NR4A3 TCF12-NR4A3 HSPA8-NR4A3

t(9;22)(q31;q12) t(9;17)(q31;q12) t(9;3)(q31;q12) t(9;15)(q31;q21) t(9;11)(q31;q24)

Desmoplastic small round cell tumour EWSR1-WT1 t(11;22)(p13;q12)

Ewing sarcoma and Ewing-like sarcomas EWSR1-FLI1

EWSR1-ERG FUS-ERG EWSR1-ETV1 EWSR1-ETV4 EWSR1-FEV EWSR1-NFATC2

EWSR1-PATZ1 EWSR1-SMARCA5

EWSR1-POU5F1 EWSR1-SP3

FUS-FEV CIC-DUX4 CIC-FOXO4 BCOR-CCNB3

FUS-NCATc2

t(11;22)(q24;q12) t(21;22)(q22;q12) der(21)t(16;21) t(7;22)(p21;q12) t(17;22)(q21;q12)

t(2;22)(q35;q12) t(20;22)(q13;q12)

inv(22) (q12q12) t(4;22) (q31;q12) t(6;22) (p21;q12) t(2;22)(q31;q12) t(2;16)(q35;p11) t(4;19)(q35;q13) t(X;19)(q13;q13) inv(X)(p11.4p11.22)

t(16;20) (p11;q13)

Perivascular epithelioid cell tumours SFPQ-TFE3 t(X;1)(p11;p34)

Soft tissue chondroma HMGA2-LPP t(3;12)(q28;214)

Mesenchymal chondrosarcoma HEY1-NCOA2

IRFBP2-CDX1

del(8)(q13;q21) t(1;5)(q42;q32)

Epithelioid haemangioma ZFP36-FOSB t(19;19)(q13.32;q13.2)

Epithelioid haemangioendothelioma WWTR1-CAMTA1

YAP1-TFE3

t(1;3)(p36;q25) t(x;11)(p11;q22) Pseudomyogenic (epithelioid sarcoma-like) haemangioendothelioma SERPINE1-FOSB t(7;19)(q22;q13)

Angiosarcoma CIC-LEUTX t(19;19)(q13.11;q13.2)

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Liposarcomas are divided into several subgroups that differ in clinical course and molecular perturbations. At present, liposarcomas are classified as well-differentiated, dedifferentiated, diversified, mucoid, round cell, and multiform.

Well-differentiated/atypical liposarcoma (WDLS) Approximately 80% of atypical liposarcomas are characterised by the presence of additional ring or giant marker chromosomes that contain amplified material in the region 12q13-15. This fragment can have vari- able length and contains genes like MDM2, TSPAN31, CDK4, HMGA2, CPM, and FRS2 [9]. The MDM2 and CDK4 proteins are involved in cell cycle regulation

— MDM2 by binding to the p53 protein and inhibiting its function and CDK4 by stimulating the phosphoryla- tion of the RB protein [9].

The 1q21-22 region including COAS and PRUNE oncogenes is also often amplified [10]. PRUNE is a nega- tive regulator of the nm23-H1 metastasis suppressor protein, and its amplification leads to a decrease in the level of free nm23-H1 and subsequently increased proliferation and migration of cells [11]. Moreover, in some cases of WDLS co-amplifications of 12q21-22 were also observed [12].

Dedifferentiated liposarcoma (DDLS)

Dedifferentiated liposarcoma is considered to be a more aggressive form derived from well-differentiated liposarcoma, and it is similarly characterised by the presence of additional giant marker and ring chromosomes. DDLS is characterised by more copy number alterations (CNAs) than WDLS — 21% and 5.7%, respectively [13]. Among the numerous chromosome disorders, the most common is amplification of the 12q13-1 region containing the MDM2 gene and a few rarer co-amplifications, among others 1q32 and 6q23, within which the JUN and ASK1 genes are located [9, 14]. In the majority of cases where MDM2 amplifica- tion is found, p53 gene mutations are absent, which distinguishes dedifferentiated liposarcoma from other high-grade sarcomas [15]. It is also believed that activation of JUN signalling pathway may be involved in the progression of WDLS to DDLS [16].

An important mechanism involved in the dediffe- rentiation of WDLS into DDLS is the inhibition or com- plete blocking of adipogenesis in which LIPE, PLIN,

FOXF2, SOX11), and cell cycle control (MAPK1, CDC2, CCNB2) differs significantly between DLLS and WDLS and may be involved in the dedifferentia- tion process [18].

Myxoid and round cell liposarcoma

The main chromosomal aberration in myxoid and round cell liposarcoma is t(12; 16)(q13; p11) translocation, which occurs in over 90% of cases [14, 19]. This translocation leads to fusion of CHOP (DDIT3) and TLS (FUS) genes located on chromosomes 12 and 16, respectively [20]. The presence of TLS-CHOP is a highly specific marker, not present in other subtypes of myxoid sarcomas [14]. The CHOP gene encodes a nuclear protein belonging to the C/EBP transcription factor family and is involved in the differentiation of adipocytes, erythropoiesis, and neoplastic transforma- tion. The TLS gene encodes a nuclear RNA-binding protein that reacts with serine-arginine proteins involved in RNA splicing [14]. During the translocation, a joining of TLS gene transcription activating domain with the leucine zipper domain CHOP occurs. The resulting fusion protein leads to a change in the level of transcription of many genes, adipogenesis inhibition, and stimulation of cell proliferation resulting in tumour formation [21]. Due to the high homology of TLS and EWS genes, in rare cases (5–10%) a t(12;

22)(q13; q12) translocation is revealed, leading to CHOP and EWS gene fusions [22]. TLS-CHOP and EWS-CHOP translocations can be detected not only on the chromosomal level by FISH, but also at the transcript level using RT-PCR. To date, 11 variants of TLS-CHOP transcripts have been identified, the most common of which are type 2 (exon 5 TLS and 2 CHOP, approximately 66%), type 1 (exon 7 TLS and 2 CHOP), and type 3 (exon 8 TLS and 2 CHOP) [14, 23]. Furthermore, fusion mRNA can also be detected in the blood [24].

Apart from the specific gene fusions in 14–18% of MLPS cases activating mutation in PIK3CA gene or ho- mozygous loss of PTEN gene are observed (the product of the latter is an inhibitor of the PIK3CA pathway).

They lead to the activation of the PI3K/AKT signalling pathway and to excessive proliferation and increased cell invasiveness. A similar effect is observed in the case of overexpression of insulin-like growth factor type 2 (IGF2) and type 1 receptor (IGFR1) [25]. Telomerase reactivation observed in 39% of cases also contributes to MLS pathogenesis [26].

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Table 2. Mutations and translocations GeneDamage typeDiagno- stic value Genetic disordersDescription of the translo- cation or mutation

TumourThe function of the wild-type geneMechanistic roleIncidence ALKTranslocationYesTPM3-ALK fusiont(1;2) (q22;p23)Inflammatory myofibroblastic tumour Receptor tyrosine kinase; participates in the development of the nervous system

The fusion leads to the formation of a constitutively active kinaseALK translocations are present in 50% of IMT ALKTranslocationYesTPM4-ALK fusiont(2; 19) (p23; p13)Inflammatory myofibroblastic tumour

Receptor tyrosine kinase; participates in the development of the nervous system

The fusion leads to the formation of a constitutively active kinaseALK translocations are present in 50% of IMT ALKTranslocationYesCLTC-ALK fusiont(2; 17) (p23; q23)Inflammatory myofibroblastic tumour

Receptor tyrosine kinase participates in the development of the nervous system The exact mechanism of action is unknown; probably the fusion leads to the formation of a tyrosine kinase with increased activity

ALK translocations are present in 50% of IMT ALKTranslocationYesRANBP2-ALK fusiont(2; 2) (p23; q13)Inflammatory myofibroblastic tumour

ALK translocations are present in 50% of IMT ALKTranslocationYesATIC-ALK fusiont(2; 2) (p23; q35)Inflammatory myofibroblastic tumour

ALK translocations are present in 50% of IMT ALKTranslocationYesCARS-ALK fusiont(2; 11) (p23; p15)Inflammatory myofibroblastic tumour

ALK translocations are present in 50% of IMT ALKTranslocationYesSEC31L1-ALK fusiont(2; 4) (p23; q21)Inflammatory myofibroblastic tumour

ALK translocations are present in 50% of IMT ALKTranslocationYesPPFIBP1-ALK fusiont(2; 12) (p23; p12)Inflammatory myofibroblastic tumour

ALK translocations are present in 50% of IMT ALKTranslocationYesRRBP1-ALK fusion?Inflammatory myofibroblastic tumour

ALK translocations are present in 50% of IMT APCMutationYes?Point mutation/ /microdeletion

VariousDesmoid tumourIt controls the expression of beta-cateninThe function of the Wnt pathway is disrupted10% BCORTranslocationYesBCOR- -CCNB3 fusionInv (X) (p11p11)BCOR-rearranged sarcomaIt participates in the regulation of apoptosis routesPerturbations in the programmed cell death pathway; dedifferentiationNA

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Table 2 (cont). Mutations and translocations GeneDamage typeDiagno- stic value Genetic disordersDescription of the translo- cation or mutation

TumourThe function of the wild-type geneMechanistic roleIncidence BCORTranslocationYesBCOR- -MAML3 fusion?BCOR-rearranged sarcomaIt participates in the regulation of apoptosis routesDisorders in the programmed cell death pathway; dedifferentiationNA BCORTranslocationYesZC3H7B-BCOR fusion?BCOR-rearranged sarcomaIt participates in the regulation of apoptosis routesDisorders in the programmed cell death pathway; dedifferentiationNA BCORTranslocationYesZC3H7B-BCOR fusiont(X; 22) (p11; q13)Endometrial stromal sarcoma, high grade

It participates in the regulation of apoptosis routesDisorders in the programmed cell death pathway; dedifferentiationNA BRAFMutationNo?Point mutationV600GISTSerine-threonine kinase in the RAS/MAPIncreases the activity of the RAS/MAP pathwayRarely CCBL1TranslocationNoCCBL1-ARL1t (9; 12) (q34; q23)Myxofibro- sarcomaKynurenine-oxoglutarate transaminaseThe exact mechanism of action is unknownNA CDK4DuplicationYesAmplification 12q13-15Amplification 12q13-15Dedifferentiated liposarcomaTakes part in the control of the cell cyclePromotes cell division100% CDX1TranslocationNoIRFBP2-CDX1t(1; 5) (q42; q32)Mesenchymal chondrosarcomaTranscription factor taking part among others in the development of the heart and intestines The exact function unknown, perhaps contributes to oncogenesis by inhibiting the p53 protein

NA CICTranslocationYesCIC-DUX4 fusiont(4; 19) (q35; q13) or t(10; 19) (q26; q13)

CIC-rearranged sarcomaTranscriptional repressor; participates in the development of the central nervous system Transition from the transcription repressor function to the factor that stimulates this process

NA CICTranslocationYesCIC-FOXO4 fusiont(X; 19) (q13; q13.3)CIC-rearranged sarcomaTranscriptional repressor participates in the development of the central nervous system

Function unknownRarely CSF1TranslocationYesCSF1-COL6A3 fusiont(1; 2) (p13; q35)Tenosynovial giant cell tumourA factor that stimulates the formation of macrophage colonies Overexpression of CSF1 causes massive infiltration of tumour mass by macrophages and its growth

25% CTNNB1MutationYes?Point mutationT41ADesmoid tumourEncodes beta-catenin, a protein responsible for intercellular adhesion and participates in the Wnt signalling pathway

The function of the Wnt pathway is disrupted85% DDIT3 (CHOP)TranslocationYesFUS-DDIT3 mergert(12; 16) (q13; p11)Myxoid liposarcomaProapoptotic transcription factorPerturbations in the programmed cell death pathway95%

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TumourThe function of the wild-type geneMechanistic roleIncidence DDIT3 (CHOP)TranslocationYesEWSR1- -DDIT3 mergert(12; 22) (q13; q12)Myxoid liposarcomaProapoptotic transcription factorDisorders in the programmed cell death pathwayRarely EEDMutationNoPoint mutation/ /microdeletion

EED inactivationMalignant peripheral nerve sheath tumour

Takes part in the organisation of chromatinIt leads to increased activity of the RAS/MAP pathway30% EWSR1TranslocationYesEWSR1-ATF1 fusiont(12; 22) (q13; q12)Clear cell sarcomaThe exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factor90% EWSR1TranslocationYesCREB1-EWSR1 fusiont(2; 22) (q32.3; q12)Clear cell sarcomaThe exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factorRarely EWSR1TranslocationYesEWSR1-WT1 mergert(11; 22) (p13; q12)Desmoplastic small round cell tumour

The exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factor75% EWSR1TranslocationYesEWSR1-FLI1 fusiont(11; 22) (q24; q12)Ewing sarcoma/PNETThe exact function is unknown; it encodes a protein binding to RNA Chimeric transcription factor that stimulates cell division, perhaps less active than other mutations in ESFT

85% EWSR1TranslocationYesEWSR1-ERG mergert(21; 22) (q12; q12)Ewing sarcoma/PNETThe exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factor10% EWSR1TranslocationYesEWSR1-ETV1t(7; 22) (p24; q12)Ewing sarcoma/PNETThe exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factorRarely EWSR1TranslocationYesEWSR1-E1AFt(17; 22) (q12; q12)Ewing sarcoma/PNETThe exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factorRarely EWSR1TranslocationYesFEV-EWSR1t(2; 22) (q33; q12)Ewing sarcoma/PNETThe exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factorRarely EWSR1TranslocationYesEWSR1- -CREB3L1 fusion

t(11; 22) (p11; q12)Sclerosing epithelioid fibrosarcoma The exact function is unknown; it encodes a protein binding to RNA

Chimeric transcription factor90%

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TumourThe function of the wild-type geneMechanistic roleIncidence FOSBTranslocationYesSERPINE1- -FOSB fusion

t(7; 19) (q22; q13),Pseudomyogenic haemangioendothelioma It takes part in dimerisation with the JUN family protein, leading to the formation of a transcription factor regulating cell division and differentiation

It leads to overexpression of FOSBNA FUSTranslocationYesFUS-CREB3L1t(11; 16) (p13; p11)Sclerosing epithelioid fibrosarcoma

Takes part in DNA repair processesChimeric transcription factor, as a result of its action, the expression of genes controlled by CREB3L1 is disturbed

Rarely FUSTranslocationYesFUS-CREB3L2 fusiont(7; 16) (q33; p11)Sclerosing epithelioid fibrosarcoma

Takes part in DNA repair processesChimeric transcription factor, as a result of its action, expression of genes controlled by CREB3L2 is disturbed

Rarely FUSTranslocationYesFUS-CREB3L2 fusiont(7; 16) (q33; p11)Fibromyxoid sarcoma, low grade

Takes part in DNA repair processesChimeric transcription factor, as a result of its action, the expression of genes controlled by CREB3L1 is disturbed

50% FUSTranslocationYesFUS-CREB3L1t(11; 16) (p11; p11)Fibromyxoid sarcoma, low grade

Takes part in DNA repair processesChimeric transcription factor, as a result of its action, expression of genes controlled by CREB3L2 is disturbed

Rarely GLITranslocationNoGLI-ACTBt(7; 12) (p22; q13-15)PericytomaEncodes the effector protein in the Hedgehog signalling pathway

Overexpression of the GLI factorNA HEY1TranslocationYesHEY1- -NCOA2 fusiont (8; 8) (q13; q21)Mesenchymal chondrosarcomaA transcription factor induced by stimulation of the NOTCH pathway It inhibits apoptosis, stimulates proliferation and the transition of cells from the epithelial to the mesenchymal form

80% HMGA2DuplicationNoAmplification 12q13-15Amplification 12q13-15Dedifferentiated liposarcomaIt participates in the differentiation of connective and fatty tissue

It leads to disorders in the differentiation of adipocytes100% IDH1MutationYes?Point mutationR132ChondrosarcomaIt metabolises isocitrate to alpha-ketoglutarate in the Krebs cycle

It causes the transition of alpha-ketoglutarate to 2-hydroxyglutarate21% IDH2MutationYes?Point mutationR172ChondrosarcomaIt metabolises isocitrate to alpha-ketoglutarate in the Krebs cycle It causes the transition of alpha-ketoglutarate to 2-hydroxyglutarate15%

(10)

TumourThe function of the wild-type geneMechanistic roleIncidence IDH2MutationYes?Point mutationR140ChondrosarcomaIt metabolises isocitrate to alpha-ketoglutarate in the Krebs cycle

It causes the transition of alpha-ketoglutarate to 2-hydroxyglutarateRarely MBTD1TranslocationYesMBTD1- -CXorf67 fusion

t(X; 17) (p11; q21)Endometrial stromal sarcoma, low grade The exact function is unknown; participates in embryonic development The exact function is unknown; probably deregulates transcription processes by disrupting chromatin remodelling

Rarely MDM2DuplicationYesAmplification 12q13-15Amplification 12q13-15Dedifferentiated liposarcomaIt inhibits the action of p53 proteinIt leads to a significant reduction in p53 activity100% NAB2TranslocationYesNAB2- -STAT6 mergerInv (12) (q13q13)Solitary fibrous tumourNAB2 is a repressor of transcription; STAT6 is its activator

As a result of gene fusions, a transcriptional activating protein is formed in regions usually inhibited by NAB2

55% NCOA2TranslocationNoSRF-NCOA2t(6; 8) (p21; q13)Spindle cell rhabdomyosarcoma

Transcription co-activator for many nuclear receptors; histone acetyltransferase activity The exact mechanism is unknown; probably leads to a perturbation of gene expression responsible for the differentiation of muscle cells

NA NCOA2TranslocationNoTEAD1-NCOA2t(8; 11) (q13; p15)Spindle cell rhabdomyo - sarcoma

Transcription co-activator for many nuclear receptors; histone acetyltransferase activity The exact mechanism is unknown; probably leads to a perturbation of gene expression responsible for the differentiation of muscle cells

NA NF1MutationNoPoint mutationNF1 inactivationGISTIt negatively regulates the RAS/MAP kinase pathwayDisturbances in the functioning of neurofibromin 1 lead to increased activity of the RAS/MAP pathway

Rarely NF1MutationYesPoint mutation/ /microdeletion

NF1 inactivationMalignant peripheral nerve sheath tumour It negatively regulates the RAS/MAP kinase pathwayDisturbances in the functioning of neurofibromin 1 lead to increased activity of the RAS/MAP pathway

88% NR4A3TranslocationYesEWSR1- -NR4A3 fusiont(9; 22) (q22; q12)Extraskeletal myxoid chondrosarcoma

Transcription factor participates in the control of cell division, differentiation and apoptosis

Modifies RNA post-translational processing75% NR4A3TranslocationYesTAF2N- -NR4A3 fusiont(9; 17) (q22; q11)Extraskeletal myxoid chondrosarcoma

The exact significance is unknownRarely

(11)

TumourThe function of the wild-type geneMechanistic roleIncidence NR4A3TranslocationYesTCF12- -NR4A3 fusiont(9; 15) (q22; q21)Extraskeletal myxoid chondrosarcoma Transcription factor participates in the control of cell division, differentiation and apoptosis

The exact significance unknownRarely NR4A3TranslocationYesTFG- -NR4A3 fusiont(3; 9) (q11; q22)Extraskeletal myxoid chondrosarcoma

The exact significance unknownRarely NR4A3TranslocationYesRBP56- -NR4A3 fusiont(9; 17) (q22; q11)Extraskeletal myxoid chondrosarcoma

The exact significance unknown20% NTRK3TranslocationYesETV6- -NTRK3 fusiont(12; 15) (p13; Q25)Fibrosarcoma, neonatal formReceptor tyrosine kinase; it promotes the survival and differentiation of neurons

It probactly leads to deregulation of the signal transduction in the NTRK3 signal pathNA NUDT11TranslocationNoKIAA2026- -NUDT11t(9; X) (p24; p11)Myxofibro- sarcomaPhosphataseThe exact mechanism of action is unknownNA PAX3TranslocationYesPAX3- -FOXO1 (FKHR) fusion

t(2; 13) (q35; q14)Alveolar rhabdomyosarcoma Transcription factor taking part among others in the development and differentiation of nervous and muscular tissue The fusion gene acts as a PAX3-like transcription factor, but with increased potency; the differentiation towards muscle tissue is disturbed

75% PAX3TranslocationYesPAX3- -NCOA1 fusiont(2; 2) (q35; p23)Alveolar rhabdomyosarcoma

Transcription factor taking part, among others, in the development and differentiation of nervous and muscular tissue

The fusion gene acts as a PAX3-like transcription factor, but with increased potencyRarely PAX3TranslocationYesPAX3-AFX fusiont(X; 2) (q35; q13)Alveolar rhabdomyosarcoma

The fusion gene acts as a PAX3-like transcription factor, but with increased potencyRarely PAX3TranslocationYesPAX3-MAML3t(2; 4) (q35; q31.1)Biphenotypic sinonasal sarcoma

Transcription factor taking part, among others, in the development and differentiation of nervous and muscular tissue The fusion gene acts as a PAX3-like transcription factor, but with increased potency79%

(12)

TumourThe function of the wild-type geneMechanistic roleIncidence PAX3TranslocationYes?PAX3-NCOA1t(2; 2) (q35; p.23)Biphenotypic sinonasal sarcoma Transcription factor taking part, among others, in the development and differentiation of nervous and muscular tissue

The fusion gene acts as a PAX3-like transcription factor, but with increased potencyRarely PAX3TranslocationYes?PAX3-FOXO1t(2; 13) (q35; q14)Biphenotypic sinonasal sarcoma

The fusion gene acts as a PAX3-like transcription factor, but with increased potencyRarely Pax7TranslocationYesPAX7- -FOXO1 (FKHR) fusion

t(1; 13) (p36; q14)Alveolar rhabdomyosarcoma

A transcription factor, highly homologous to PAX3The fusion gene acts as a PAX3-like transcription factor, but with increased potency10% PDGFBTranslocationYesCOL1A1- -PDGFB fusionRing form of chromosomes 17 and 22

Dermatofibro- sarcoma protuberans Isoform of platelet derived growth factor, essential in the process of angiogenesis The fusion protein retains PDGFB-stimulating properties and stimulates tumour cells for development

75% PDGFRAMutationYesPoint mutationD842VGISTReceptor tyrosine kinase stimulation stimulates cells to grow and divide as a result of stimulation by platelet-derived growth factor

Constitutional kinase activation without the need for ligand6% PHF1TranslocationYesPHF1- -JAZF1 fusiont(6; 7) (p21; 7p15)Endometrial stromal sarcoma, low grade

Takes part in the regulation of gene expression by changing the chromatin structure The exact function is unknown; probably deregulates transcription processes by disrupting chromatin remodelling

50% PHF1TranslocationYesEPC1-PHF1 fusiont(6; 10) (p21; p11)Endometrial stromal sarcoma, low grade

Rarely PHF1TranslocationYesMEAF6- -PHF1 fusiont(1; 6) (p34; p21)Endometrial stromal sarcoma, low grade

Rarely PHF1TranslocationNoAFF3-PHF1t(2; 6) (q12; p21)Myxofibro- sarcomaTakes part in the regulation of gene expression by changing the chromatin structure

The exact function is unknown; probably deregulates transcription processes by disrupting chromatin remodelling

NA

(13)

TumourThe function of the wild-type geneMechanistic roleIncidence ROS1TranslocationYesTFG-ROS1 merger?Inflammatory myofibroblastic tumour A receptor tyrosine kinase with a similar structure to ALK; exact function unknown The exact mechanism of action is unknown, probably the fusion leads to the formation of a tyrosine kinase with increased activity

Rarely ROS1TranslocationYesYWHAE- -ROS1 fusion?Inflammatory myofibroblastic tumour

A receptor tyrosine kinase with a similar structure to ALK; exact function unknown The exact mechanism of action is unknown, probably the fusion leads to the formation of a tyrosine kinase with increased activity

Rarely SDHB/ /SHDC/ /SDHD

MutationNoPoint mutationVariousGISTSuccinate dehydrogenase (SDH) subunit, an enzyme involved in the process of cellular respiration SDH deficiency probably leads to oxidative stress and to increased stimulation of cell growth by IGF and VEGF

5% SMARCB1TranslocationYesSMARCB1 inactivationDelegation 22qRhabdoid tumourTakes part in chromatin remodellingThe lack of activity of SMARCB1 leads to dysregulation of the cell cycle35% SMARCB1TranslocationYesSMARCB1 inactivationDelegation 22qEpithelioid sarcomaTakes part in chromatin remodellingThe lack of activity of SMARCB1 leads to dysregulation of the cell cycleTotal 90–95% SMARCB1TranslocationYesSMARCB1 inactivationt(8; 22) (q22; q11)Epithelioid sarcomaTakes part in chromatin remodellingThe lack of activity of SMARCB1 leads to dysregulation of the cell cycleTotal 90–95% SMARCB1TranslocationYesSMARCB1 inactivationt(10; 22)Epithelioid sarcomaTakes part in chromatin remodellingThe lack of activity of SMARCB1 leads to dysregulation of the cell cycleTotal 90–95% SS18TranslocationYesSS18-SSX1t(X; 22) (p11.23; q11)Synovial sarcomaTranscription factorThe exact function is unknown; it may interfere with cell differentiation by affecting epigenetic factors

60–70% monophasic, 30–40% biphasic SS18TranslocationYesSS18-SSX2t(X; 18) (p11.21; q11)Synovial sarcomaTranscription factorThe exact function is unknown; it may interfere with cell differentiation by affecting epigenetic factors

97% monophasic, 3% biphasic SS18TranslocationYesSS18-SSX4t(X; 18) (p11; q11)Synovial sarcomaTranscription factorThe exact function is unknown; it may interfere with cell differentiation by affecting epigenetic factors

Rarely SS18LTranslocationYesSS18L-SSX1t(X; 20) (p11; q13)Synovial sarcomaTranscription factorThe exact function is unknown; it may interfere with cell differentiation by affecting epigenetic factors

Rarely

(14)

TumourThe function of the wild-type geneMechanistic roleIncidence SUZ12TranslocationYesJAZF1-SUZ12 fusiont(7; 17) (p15; q21)Endometrial stromal sarcoma, low grade Participates in the regulation of embryonic developmentIt causes the constitutive expression of a chimeric protein with antiapoptotic properties

30% SUZ12MutationNoPoint mutation/ /microdeletion

SUZ12 inactivationMalignant peripheral nerve sheath tumour

It participates in the regulation of embryonic developmentIt leads to increased activity of the RAS/pathway50% TFE3TranslocationYesTFE3-ASPSCR1 fusiont(X; 17) (p11.2; Q25)Alveolar soft part sarcomaBoth TFE3 and ASPSCR1 are transcription factorsAs a result of translocation, a transient transcription factor that promotes oncogenesis is formed

99% TFE3TranslocationYesYAP1-TFE3 fusiont(X; 11) (p11; q22)Epithelioid haemangioendothelioma

Transcription factorThe exact significance unknown; the function of the Hippo pathway is probably disrupted22% WWTR1TranslocationYesWWTR1- -CAMTA1 fusion

t(1; 3) (p36; Q25)Epithelioid haemangioendothelioma It participates in the control of the size of internal organs, a pro-apoptotic factor

The exact function is unknown~55% YWHAETranslocationYesYWHAE- -NUTM2A fusion

t(10; 17) (q22; p13)Endometrial stromal sarcoma, high grade A signalling protein from the family 14-3-3, probably involved in the regulation of cell division

The exact function is unknownup to 26%